I strongly recommend reading literature on REMD and following procedures in
similar work.
The number of replicas scales with system size- it isn't the sq root
directly. There are many ways to calculate number of replicas, most
depending on the potential energy of the system and how is scales with
temperature.
It's not clear to me how a protein-DNA complex is only 2688 atoms. If you
can be more specific about exactly what you are doing we may be able to help
more.
On Sat, Dec 25, 2010 at 7:53 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Hello all
>
> I have a modelled protein - DNA complex in protein C-terminus has 16
> residues
> radom coil.
> It is hypothesized that this region folds into a alpha helix when bound to
> DNA.So here I
> want to use REMD.It has total 2688 atoms as first step is to determine
> number of
> replicas.
> As according to amber tutorial :-
> http://ambermd.org/tutorials/advanced/tutorial7/
> number of replica is determine according to square root of number of total
> atoms, as my
> sytem have total 2688 atoms and its square root is ~51 so should I consider
> number of replica
> 51?
>
> So kindly suggest me.
>
> With regard
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
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Received on Sat Dec 25 2010 - 09:00:02 PST
